This directory contains compressed FASTA alignments for the CDS regions
of the rat genome (rn4, Nov. 2004) aligned to the following assemblies:

  - mouse (Feb 2006, mm8)
  - human (Mar 2006, hg18) 
  - dog (May 2005, canFam2) 
  - cow (Mar 2005, bosTau2) 
  - opossum (Jan 2006, monDom4) 
  - chicken (Feb 2004, galGal2) 
  - frog (Oct 2004, xenTro1) 
  - zebrafish (May 2005, danRer3) 


Files included in this directory:
  - refGene.exon*.fa.gz: for each exon in the Baylor 3.4/rn4 RefSeq Gene  track,
    this file contains either amino acids (AA) or nucleotides (Nuc) for
    Baylor 3.4/rn4 and the aligning genomes.
  - rgdGene2Canonical.exon*.fa.gz: for each exon in the Baylor 3.4/rn4 
    canonical set of RGD Genes 2, this file contains either amino acids (AA) 
    or nucleotides (Nuc) for Baylor 3.4/rn4  and the aligning genomes.
  - rgdGene2.exon*.fa.gz: for each exon in the Baylor 3.4/rn4 RGD Genes 2 track,
    this file contains either amino acids (AA) or nucleotides (Nuc) for
    Baylor 3.4/rn4 and the aligning genomes.

For a description of multiple alignment format (MAF), see
http://genome.ucsc.edu/goldenPath/help/maf.html
and http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#FASTA.

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To download a large file or multiple files from this directory, we recommend 
that you use ftp rather than downloading the files via our website. To do so: 
    ftp hgdownload.cse.ucsc.edu 
    user name: anonymous
    password: <your email address>
    go to the directory goldenPath/hg19/multiz46way/alignments

To download multiple files from the UNIX command line, use the "mget" command. 
    mget <filename1> <filename2> ...
    - or -
    mget -a (to download all the files in the directory) 
Use the "prompt" command to toggle the interactive mode if you do not want 
to be prompted for each file that you download.

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All the files in this directory are freely usable for any 
purpose. For data use restrictions regarding the individual 
genome assemblies, see http://genome.ucsc.edu/goldenPath/credits.html.